February 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] e29926: Updates for the zfs admin module
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e2992640880d0df95df4256a16219e4059bbb90a https://github.com/galaxyproject/infrastructure-playbook/commit/e2992640880… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M common_roles M env/galaxy/host_vars/orval.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml Log Message: ----------- Updates for the zfs admin module

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[galaxyproject/galaxy] 6070bf: simplify Webhooks' structure
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6070bf07e18b0d3ebc210f3c4c44a1ed14b1dd27 https://github.com/galaxyproject/galaxy/commit/6070bf07e18b0d3ebc210f3c4c44… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css Log Message: ----------- simplify Webhooks' structure Commit: ada76931d8231a83ff15667ccec652b06bd793d4 https://github.com/galaxyproject/galaxy/commit/ada76931d8231a83ff15667ccec6… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M lib/galaxy/webhooks/__init__.py Log Message: ----------- add weighted random webhook pick Commit: 90d59ac9234d7a756eb3040cccb35c6e181826ec https://github.com/galaxyproject/galaxy/commit/90d59ac9234d7a756eb3040cccb3… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M test/api/test_webhooks.py M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- fix webhooks tests Commit: 57c1fc78043220ec16081255c2b15e854cac976c https://github.com/galaxyproject/galaxy/commit/57c1fc78043220ec16081255c2b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js Log Message: ----------- Client formatting of webhooks changes. Commit: 0ac7b7830dd06ef474002a57c677ca429913d766 https://github.com/galaxyproject/galaxy/commit/0ac7b7830dd06ef474002a57c677… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/webhooks/__init__.py Log Message: ----------- Fix import order in webhooks/__init__.py Commit: 3b7daece0460286288a8678c5020dd6530d5457f https://github.com/galaxyproject/galaxy/commit/3b7daece0460286288a8678c5020… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/webhooks.js Log Message: ----------- Delay interpolation of webhook url template; Galaxy won't exist as a configured object necessarily when this is imported. Commit: 22b0b2f2e90249feacacd0f8cfb60a9335bb40e9 https://github.com/galaxyproject/galaxy/commit/22b0b2f2e90249feacacd0f8cfb6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/qunit/tests/page_tests.js Log Message: ----------- Minor tweaks/fixes while trying to sort out qunit test failures related to webhook changes. Commit: fa0ba22f97cbf69c30828205ea94358094b654e0 https://github.com/galaxyproject/galaxy/commit/fa0ba22f97cbf69c30828205ea94… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/qunit/test-app.js Log Message: ----------- Fix webhook filtering, make it a bit more defensive. Minor other tweaks. Commit: 9b4465efd37fe7c27276971a2348283e41cc9027 https://github.com/galaxyproject/galaxy/commit/9b4465efd37fe7c27276971a2348… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/menu.js Log Message: ----------- fix webhook's property name Commit: 29c766167a64f302341101b0a7301fcd29634698 https://github.com/galaxyproject/galaxy/commit/29c766167a64f302341101b0a730… Author: Evgeny Anatskiy <evgeny.anatskiy(a)gmail.com> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/special_topics/webhooks.rst Log Message: ----------- update webhooks docs Commit: ffaabe0a63f47c57cd9785de84cf9e77e398b95c https://github.com/galaxyproject/galaxy/commit/ffaabe0a63f47c57cd9785de84cf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/mvc/history/options-menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M client/galaxy/scripts/qunit/test-app.js M client/galaxy/scripts/qunit/tests/page_tests.js A config/plugins/webhooks/demo/search/config.yml R config/plugins/webhooks/demo/search/config/searchover.yaml A config/plugins/webhooks/demo/search/script.js R config/plugins/webhooks/demo/search/static/script.js R config/plugins/webhooks/demo/search/static/styles.css A config/plugins/webhooks/demo/search/styles.css A config/plugins/webhooks/demo/tool_list/__init__.py A config/plugins/webhooks/demo/tool_list/config.yml R config/plugins/webhooks/demo/tool_list/config/tool_list.yml R config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/__init__.py A config/plugins/webhooks/demo/tour_generator/config.yml R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml R config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/script.js R config/plugins/webhooks/demo/tour_generator/static/script.js R config/plugins/webhooks/demo/tour_generator/static/styles.css A config/plugins/webhooks/demo/tour_generator/styles.css M doc/source/admin/special_topics/webhooks.rst M lib/galaxy/webapps/galaxy/api/webhooks.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webhooks/__init__.py M test/api/test_webhooks.py A test/functional/webhooks/history_test1/config.yml R test/functional/webhooks/history_test1/config/history_test1.yml A test/functional/webhooks/history_test2/config.yml R test/functional/webhooks/history_test2/config/history_test2.yml A test/functional/webhooks/masthead_test/config.yml R test/functional/webhooks/masthead_test/config/masthead_test.yml A test/functional/webhooks/phdcomics/__init__.py A test/functional/webhooks/phdcomics/config.yaml R test/functional/webhooks/phdcomics/config/phdcomics.yaml R test/functional/webhooks/phdcomics/helper/__init__.py A test/functional/webhooks/phdcomics/script.js R test/functional/webhooks/phdcomics/static/script.js R test/functional/webhooks/phdcomics/static/styles.css A test/functional/webhooks/phdcomics/styles.css A test/functional/webhooks/trans_object/__init__.py A test/functional/webhooks/trans_object/config.yaml R test/functional/webhooks/trans_object/config/trans_object.yaml R test/functional/webhooks/trans_object/helper/__init__.py A test/functional/webhooks/xkcd/config.yml R test/functional/webhooks/xkcd/config/xkcd.yml A test/functional/webhooks/xkcd/script.js R test/functional/webhooks/xkcd/static/script.js R test/functional/webhooks/xkcd/static/styles.css A test/functional/webhooks/xkcd/styles.css M test/selenium_tests/test_tool_describing_tours.py Log Message: ----------- Merge pull request #5342 from dannon/integration.webhooks_improvements [18.01] Webhooks improvements Compare: https://github.com/galaxyproject/galaxy/compare/a37b638491bc...ffaabe0a63f4

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[galaxyproject/galaxy] 6bdd75: WIP framework dependencies doc update
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 6bdd755aafbb008422db46231949ad3c6e4e608f https://github.com/galaxyproject/galaxy/commit/6bdd755aafbb008422db46231949… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- WIP framework dependencies doc update Commit: fd96864bd6fca8f4ff149ca0ba270ebb164254ac https://github.com/galaxyproject/galaxy/commit/fd96864bd6fca8f4ff149ca0ba27… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-25 (Thu, 25 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Finish updates to framework dependencies doc Commit: 6333e83a6517830599d17e42707f0bead367d135 https://github.com/galaxyproject/galaxy/commit/6333e83a6517830599d17e42707f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-01-26 (Fri, 26 Jan 2018) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Doc corrections from @nsoranzo Commit: a37b638491bc1d04be266bf9a14852fcfb62c342 https://github.com/galaxyproject/galaxy/commit/a37b638491bc1d04be266bf9a148… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M doc/source/admin/framework_dependencies.rst M doc/source/admin/scaling.md R lib/galaxy/dependencies/conda-environment.txt A lib/galaxy/dependencies/conda-file.sh M scripts/common_startup.sh Log Message: ----------- Merge pull request #5390 from natefoo/framework-dependencies-doc-update [18.01] Update framework dependencies documentation Compare: https://github.com/galaxyproject/galaxy/compare/6b0542f7c287...a37b638491bc

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[galaxyproject/infrastructure-playbook] dbabd0: Backup Main public libraries
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/galaxyenv Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dbabd0075f3a25a94bb930e805e55531fe96c5bf https://github.com/galaxyproject/infrastructure-playbook/commit/dbabd0075f3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M common_roles M env/galaxy/group_vars/sshservers/vault.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vars.yml M env/galaxy/host_vars/westvleteren.galaxyproject.org/vault.yml M env/galaxy/inventory A taccenv/group_vars/sshclients/vars.yml A taccenv/group_vars/sshclients/vault.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vars.yml A taccenv/host_vars/galaxy-web-05.tacc.utexas.edu/vault.yml M taccenv/inventory A taccenv/zfsdump-gxmain.yml Log Message: ----------- Backup Main public libraries

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[galaxyproject/galaxy] 30ac9e: Workaround for extra metadata revision creation
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 30ac9e940ac48195760d8f2970eef97a6320b52c https://github.com/galaxyproject/galaxy/commit/30ac9e940ac48195760d8f2970ee… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Workaround for extra metadata revision creation Without this change, uploading non-metadata changes to a toolshed repository will display an error message and create a new metadata revision regardless of whether the code should determine that a new metadata revision is warranted. Commit: 6b0542f7c2877557148dec8abfba6577c8f5ee11 https://github.com/galaxyproject/galaxy/commit/6b0542f7c2877557148dec8abfba… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #5433 from davebx/release_18.01 [18.01] Workaround for extra metadata revision creation Commit: a76614486be3dd0ad85f0007d604655dde02d6e9 https://github.com/galaxyproject/galaxy/commit/a76614486be3dd0ad85f0007d604… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9489fe471155...a76614486be3

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[galaxyproject/galaxy] 30ac9e: Workaround for extra metadata revision creation
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 30ac9e940ac48195760d8f2970eef97a6320b52c https://github.com/galaxyproject/galaxy/commit/30ac9e940ac48195760d8f2970ee… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Workaround for extra metadata revision creation Without this change, uploading non-metadata changes to a toolshed repository will display an error message and create a new metadata revision regardless of whether the code should determine that a new metadata revision is warranted. Commit: 6b0542f7c2877557148dec8abfba6577c8f5ee11 https://github.com/galaxyproject/galaxy/commit/6b0542f7c2877557148dec8abfba… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #5433 from davebx/release_18.01 [18.01] Workaround for extra metadata revision creation Compare: https://github.com/galaxyproject/galaxy/compare/baae416472b0...6b0542f7c287

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[galaxyproject/infrastructure-playbook] e3cb79: Add toolshed redirect to gxy.io
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: e3cb79ce021454db04c554f00373ff883d87fcd0 https://github.com/galaxyproject/infrastructure-playbook/commit/e3cb79ce021… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M galaxyenv/templates/nginx/gxy.io.j2 Log Message: ----------- Add toolshed redirect to gxy.io

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[galaxyproject/galaxy] 847d80: Cleanup per-destination container override in job ...
by GitHub 01 Feb '18

01 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 847d801c61702d826c948688b9305427d2f32ca2 https://github.com/galaxyproject/galaxy/commit/847d801c61702d826c948688b930… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-01-31 (Wed, 31 Jan 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Cleanup per-destination container override in job config. - Python 3 fix to martialize iterator into list. - Restrict XML query to just container elements - this is much more correct. Both fixes thanks to @nsoranzo. Commit: 9489fe471155c92028216ebf02056ed6389fddd4 https://github.com/galaxyproject/galaxy/commit/9489fe471155c92028216ebf0205… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-01 (Thu, 01 Feb 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #5427 from jmchilton/py3_fix Python 3 fix for reading container elements from job_conf. Compare: https://github.com/galaxyproject/galaxy/compare/db287a227441...9489fe471155

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